Re: [gmx-users] J-walking REMD

On 2/1/10 6:01 AM, Mark Abraham wrote: On 27/01/10 19:00, David Parcej wrote: Dear All Some time ago there was a discussion concerning the problems of REMD for large systems and the possibility of using the REST implementation of the method. Mark, you mentioned that you had coded an implementati

Re: [gmx-users] error: Cannot compile and link MPI code with mpicc

On 01/02/10 18:01, Chandan Choudhury wrote: Thanks. I just added export CPPFLAGS=-I/usr/local/openmpi/include in the bashrc file, and could compile the mpi version of gromacs. The next thing is I got the error on executing mdrun_mpi -h Following is the output. Kindly help. corsica:/usr/local/gro

Re: [gmx-users] Hydrogen molecule topology error

On 01/02/10 15:58, Nataraj wrote: Dear gmx-users, I would like to perform a simulation of diffusion of hydrogen molecule (H2) from surrounding water to the protein interior. In this regard, I have the information of partial charge of the hydrogen molecule from the literature so I have developed

Re: [gmx-users] error: Cannot compile and link MPI code with mpicc

Thanks. I just added export CPPFLAGS=-I/usr/local/openmpi/include in the bashrc file, and could compile the mpi version of gromacs. The next thing is I got the error on executing mdrun_mpi -h Following is the output. Kindly help. corsica:/usr/local/gromacs/bin # mdrun_mpi -h [corsica:17130] [NO-NA

[gmx-users] Hydrogen molecule topology error

Dear gmx-users, I would like to perform a simulation of diffusion of hydrogen molecule (H2) from surrounding water to the protein interior. In this regard, I have the information of partial charge of the hydrogen molecule from the literature so I have developed my own 'itp' file with an assumption

Re: [gmx-users] error: Cannot compile and link MPI code with mpicc

> > Message: 5 > Date: Sun, 31 Jan 2010 00:34:22 +0530 > From: Chandan Choudhury > Subject: Re: [gmx-users] error: Cannot compile and link MPI code with >mpicc > To: Discussion list for GROMACS users > Message-ID: ><4e22679c1001301104r5f1d725bjd5824e68cb3cb...@mail.gmail.com> > Co

Re: [gmx-users] J-walking REMD

On 27/01/10 19:00, David Parcej wrote: Dear All Some time ago there was a discussion concerning the problems of REMD for large systems and the possibility of using the REST implementation of the method. Mark, you mentioned that you had coded an implementation Okur method (JCTC, 2006, 2, 420). How

[gmx-users] rdf

Looks great to me... what's the problem? -- original message -- okay this should work http://docs.google.com/fileview?id=0B_QNmYARywUiNzE0MDA0NWMtYjFiMy00MTRjLThkNDMtNTk3NDgyNjcxZTgx&hl=en -Nisha Quoting chris.neale at utoronto.ca: I didn't get the attachment. Please upload the image to som

Re: [gmx-users] rdf

okay this should work http://docs.google.com/fileview?id=0B_QNmYARywUiNzE0MDA0NWMtYjFiMy00MTRjLThkNDMtNTk3NDgyNjcxZTgx&hl=en -Nisha Quoting chris.ne...@utoronto.ca: I didn't get the attachment. Please upload the image to some website and post the link. --original message -- I saved my r

[gmx-users] rdf

I didn't get the attachment. Please upload the image to some website and post the link. --original message -- I saved my rdf plot as a pdf file and I have attached it to this email. Hopefully it will work. My system is one methane with 893 molecules of tip3p water in a cubic box of size 3

RE: [gmx-users] rdf

A single methane molecule in water, it is not surprising at all that there is some noise in the rdf produced. If you want it smoother than that, you will simply having to run it for longer. The rdf is an average, insufficient data points mean it will be noisy, you cannot get around that fact. Ca

Re: [gmx-users] rdf

Hi, I saved my rdf plot as a pdf file and I have attached it to this email. Hopefully it will work. My system is one methane with 893 molecules of tip3p water in a cubic box of size 3 3 3 (nm). My topology file is : ; Include forcefield parameters #include "ffoplsaa.itp" [ moleculetyp

[gmx-users] mailing list search gives "Site settings could not be loaded"

I used http://www.gromacs.org/Support/Mailing_Lists/Search but it appears to be fine now... just a glitch I guess. On 1/31/10 10:25 PM, chris.neale at utoronto.ca wrote: Anybody else having trouble searching the gromacs archives? I get this message: Site settings could not be loaded We were u

Re: [gmx-users] mailing list search gives "Site settings could not be loaded"

On 1/31/10 10:25 PM, chris.ne...@utoronto.ca wrote: Anybody else having trouble searching the gromacs archives? I get this message: Site settings could not be loaded We were unable to locate the API to request site settings. Please see below for debugging information. HTTP Response Status C

[gmx-users] mailing list search gives "Site settings could not be loaded"

Anybody else having trouble searching the gromacs archives? I get this message: Site settings could not be loaded We were unable to locate the API to request site settings. Please see below for debugging information. HTTP Response Status Code: 0 -- gmx-users mailing listgmx-users@grom

[gmx-users] rdf

make a figure of your rdf, post it online somewhere (I use photobucket) and reply to the list with a link to your figure. Make sure your figure is well labeled and give us a thorough description of what you see that you don't like. Also tell us what your unit-cell box vectors are. Also desc

Re: [gmx-users] rdf

nishap.pa...@utoronto.ca wrote: Hi Will, I have been using pme from the very start and it didn't help with the volume. Could you please elaborate on what you mean by average g(r) over every molecule? And because my rdf-s are not smooth enough even with 100ns, I get fluctuating data

Re: [gmx-users] rdf

Hi Will, I have been using pme from the very start and it didn't help with the volume. Could you please elaborate on what you mean by average g(r) over every molecule? And because my rdf-s are not smooth enough even with 100ns, I get fluctuating data using rdf-s. -Nisha Quoti

[gmx-users] error: Cannot compile and link MPI code with mpicc

Looks to me like you are not linking properly to the mpi libraries. Please post your gromacs compilation commands in full. For example, mine are posted below. Note also that some clusters make it more difficult for you depending on their setup. I have used clusters in which the simplest way

Re: [gmx-users] Heating error

mohammad reaza dayer wrote: Dear Justin Greetings: I want to melt up hemoglobin, using simulated annealing methods. I used the following mdp file parameters: constraints=all-bonds integrator=md dt=0.002 ; ps ! nst

[gmx-users] Heating error

Dear Justin Greetings: I want to melt up hemoglobin, using simulated annealing methods. I used the following mdp file parameters: constraints=all-bonds integrator=md dt=0.002 ; ps ! nsteps=10 ; total 100.0 ps.